The hydrophone is an indispensable component of sonar systems for acquiring underwater acoustic information, and its inherent noise level directly impacts sonar performance. It is essential to accurately determine the equivalent noise spectrum level of a hydrophone, both during its development phase and throughout its operation and maintenance stages. This article addresses the challenge that hydrophone equivalent noise is extremely weak and its measurement process is susceptible to interference from external environmental sounds, vibrations, and electromagnetic waves. This study proposes a measurement environment construction scheme combining sound insulation, vibration reduction, and electromagnetic shielding. Building upon this well-constructed measurement environment, we further employ low-noise preamplifier circuit design and the averaged periodogram power spectrum estimation method to achieve accurate measurement of the hydrophone equivalent noise spectrum level. The article provides estimation methods for vibration reduction and electromagnetic shielding effectiveness, along with measures to effectively suppress circuit noise. A measurement system is developed using the proposed method. The sound insulation and electromagnetic shielding effectiveness of the system are tested, showing an acoustic attenuation greater than 70 dB and an electromagnetic attenuation greater than 60 dB, effectively satisfying practical requirements. The effectiveness of the averaged periodogram power spectrum estimation method is evaluated through experimental results. It is also concluded that for different measurement frequency bands, users should select appropriate total acquisition duration and segment numbers to balance measurement efficiency with accuracy. Finally, the measurement system is used to determine the equivalent noise spectrum level of the RESON TC4014 low-noise hydrophone. The results show that the experimentally obtained equivalent noise spectrum curve for the TC4014 coincides with the curve provided by the manufacturer, validating the effectiveness of the proposed method.